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/*
* mergefilecommand.cpp
* Mothur
*
* Created by Pat Schloss on 6/14/09.
* Copyright 2009 Patrick D. Schloss. All rights reserved.
*
*/
#include "mergefilecommand.h"
//**********************************************************************************************************************
vector<string> MergeFileCommand::setParameters(){
try {
CommandParameter pinput("input", "String", "", "", "", "", "","",false,true,true); parameters.push_back(pinput);
CommandParameter poutput("output", "String", "", "", "", "", "","",false,true,true); parameters.push_back(poutput);
CommandParameter pseed("seed", "Number", "", "0", "", "", "","",false,false); parameters.push_back(pseed);
CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
CommandParameter ptaxonomy("taxonomy", "", "", "", "none", "none", "none","",false,true,true); parameters.push_back(ptaxonomy);
CommandParameter pfasta("fasta", "", "", "", "none", "none", "none","taxonomy",false,true,true); parameters.push_back(pfasta);
CommandParameter pname("name", "InputTypes", "", "", "NameCount", "none", "none","",false,false,true); parameters.push_back(pname);
CommandParameter pcount("count", "InputTypes", "", "", "NameCount-CountGroup", "none", "none","",false,false,true); parameters.push_back(pcount);
abort = false; calledHelp = false; appendMode = true;
vector<string> tempOutNames;
outputTypes["merge"] = tempOutNames;
outputTypes["fasta"] = tempOutNames;
vector<string> myArray;
for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
return myArray;
}
catch(exception& e) {
m->errorOut(e, "MergeFileCommand", "setParameters");
exit(1);
}
}
//**********************************************************************************************************************
string MergeFileCommand::getHelpString(){
try {
string helpString = "";
helpString += "The merge.file command takes a list of files separated by dashes and appends them into one file. Altternatively, the merge file command can combine the data of several files. For example, you can combine a fasta, taxonomy and name or count field to achieve outputs like: GQY1XT001C44N8 3677 Bacteria;Bacteroidetes;Bacteroidia;Bacteroidales;Porphyromonadaceae;Porphyromonadaceae_unclassified; C-G--T-T--GA-A-A-C-T-G-G--CG-T-T-C--T-T-G-A-G-T-G-G-GC-GA-G-A-A-G-T-A--TG-C-GG-A-ATG-C-G-T-G-GT-GT-A-G-CGGT-G-AAA--...";
helpString += "The merge.file command parameters are input and output or fasta, taxonomy, name and count.";
helpString += "Example merge.file(input=small.fasta-large.fasta, output=all.fasta).";
helpString += "Example merge.file(fasta=final.fasta, name=final.names, taxonomy=final.taxonomy).";
return helpString;
}
catch(exception& e) {
m->errorOut(e, "MergeFileCommand", "getHelpString");
exit(1);
}
}
//**********************************************************************************************************************
string MergeFileCommand::getOutputPattern(string type) {
try {
string pattern = "";
if (type == "fasta") { pattern = "[filename],merged,[extension]"; }
else if (type == "merge") { pattern = ""; }
else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->setControl_pressed(true); }
return pattern;
}
catch(exception& e) {
m->errorOut(e, "MergeFileCommand", "getOutputPattern");
exit(1);
}
}
//**********************************************************************************************************************
MergeFileCommand::MergeFileCommand(string option) : Command() {
try {
if(option == "help") { help(); abort = true; calledHelp = true; }
else if(option == "citation") { citation(); abort = true; calledHelp = true;}
else if(option == "category") { abort = true; calledHelp = true; }
else {
OptionParser parser(option, setParameters());
map<string,string> parameters = parser.getParameters();
ValidParameters validParameter;
string inputDir = validParameter.validPath(parameters, "inputdir");
if (inputDir == "not found"){ inputDir = ""; }
string fileList = validParameter.validPath(parameters, "input");
if(fileList == "not found") { appendMode = false; fileList = ""; }
else{ util.splitAtDash(fileList, fileNames); }
outputFileName = validParameter.validPath(parameters, "output");
if (outputFileName == "not found") { appendMode = false; outputFileName = ""; }
fastafile = validParameter.validFile(parameters, "fasta");
if (fastafile == "not open") { fastafile = ""; abort = true; }
else if (fastafile == "not found") { fastafile = ""; }
else { current->setFastaFile(fastafile); appendMode = false; }
namefile = validParameter.validFile(parameters, "name");
if (namefile == "not open") { namefile = ""; abort = true; }
else if (namefile == "not found") { namefile = ""; }
else { current->setNameFile(namefile); appendMode = false; }
taxfile = validParameter.validFile(parameters, "taxonomy");
if (taxfile == "not open") { taxfile = ""; abort = true; }
else if (taxfile == "not found") { taxfile = ""; }
else { current->setTaxonomyFile(taxfile); appendMode = false; }
countfile = validParameter.validFile(parameters, "count");
if (countfile == "not open") { countfile = ""; abort = true; }
else if (countfile == "not found") { countfile = ""; }
else { current->setCountFile(countfile); appendMode = false; }
if (!appendMode) { //if you are not appending, fasta is required as well as at least one of taxonomy, name or count
if (fastafile == "") { //look for current
fastafile = current->getFastaFile();
if (fastafile != "") { m->mothurOut("Using " + fastafile + " as input file for the fasta parameter.\n"); }
else { m->mothurOut("[ERROR]: You have no current fastafile and the fasta parameter is required.\n"); abort = true; }
}
if ((namefile == "") && (countfile == "") && (taxfile == "")) {
taxfile = current->getTaxonomyFile();
if (taxfile != "") { m->mothurOut("Using " + taxfile + " as input file for the taxonomy parameter.\n"); }
else {
countfile = current->getCountFile();
if (countfile != "") { m->mothurOut("Using " + countfile + " as input file for the count parameter.\n"); }
else {
namefile = current->getNameFile();
if (namefile != "") { m->mothurOut("Using " + namefile + " as input file for the name parameter.\n"); }
else { m->mothurOut("[ERROR]: You have no current taxonomy, name or count files. At least one is required. \n"); abort = true; }
}
}
}
if ((namefile != "") && (countfile != "")) {
m->mothurOut("[ERROR]: you may only use one of the following: name or count.\n"); abort = true;
}
}else {
numInputFiles = fileNames.size();
ifstream testFile;
if(numInputFiles == 0){ m->mothurOut("you must enter two or more file names and you entered " + toString(fileNames.size()) + " file names\n"); abort=true; }
else{
for(int i=0;i<numInputFiles;i++){
string path = util.hasPath(fileNames[i]);
if (inputDir != "") {
//if the user has not given a path then, add inputdir. else leave path alone.
if (path == "") { fileNames[i] = inputDir + fileNames[i]; }
}
if (util.checkLocations(fileNames[i], current->getLocations())) { }
else { fileNames.erase(fileNames.begin()+i); i--; } //erase from file list
path = util.hasPath(fileNames[i]);
if (path != "") { if (outputdir == "") { outputdir = path; } }
}
if (outputdir != "") { outputFileName = outputdir + util.getSimpleName(outputFileName); }
}
}
}
}
catch(exception& e) {
m->errorOut(e, "MergeFileCommand", "MergeFileCommand");
exit(1);
}
}
//**********************************************************************************************************************
int MergeFileCommand::execute(){
try {
if (abort) { if (calledHelp) { return 0; } return 2; }
if (appendMode) {
util.mothurRemove(outputFileName);
for(int i=0;i<numInputFiles;i++){ util.appendFiles(fileNames[i], outputFileName); }
outputNames.push_back(outputFileName); outputTypes["merge"].push_back(outputFileName);
}else { outputFileName = mergeFileData(); }
if (m->getControl_pressed()) { util.mothurRemove(outputFileName); return 0; }
//set taxonomy file as new current taxonomyfile
string currentName = "";
itTypes = outputTypes.find("fasta");
if (itTypes != outputTypes.end()) { if ((itTypes->second).size() != 0) { currentName = (itTypes->second)[0]; current->setFastaFile(currentName); } }
m->mothurOut("\nOutput File Names: \n");
m->mothurOut(outputFileName); m->mothurOutEndLine();
m->mothurOutEndLine();
return 0;
}
catch(exception& e) {
m->errorOut(e, "MergeFileCommand", "execute");
exit(1);
}
}
//**********************************************************************************************************************
string MergeFileCommand::mergeFileData(){
try {
string thisOutputDir = outputdir;
if (outputdir == "") { thisOutputDir += util.hasPath(fastafile); }
map<string, string> variables;
variables["[filename]"] = thisOutputDir + util.getRootName(util.getSimpleName(fastafile));
variables["[extension]"] = util.getExtension(fastafile);
outputFileName = getOutputFileName("fasta", variables);
ofstream out;
util.openOutputFile(outputFileName, out);
//extract seq counts from name or count file
map<string, int> nameMap; map<string, int>::iterator itCount;
bool useNameMap = true;
if (countfile != "") {
CountTable ct; ct.readTable(countfile, false, false);
nameMap = ct.getNameMap();
}else if (namefile != "") {
nameMap = util.readNames(namefile);
}else { useNameMap = false; }
map<string, string> taxMap; map<string, string>::iterator itTax;
bool useTax = false;
if (taxfile != "") { util.readTax(taxfile, taxMap, false); useTax = true; }
ifstream in; util.openInputFile(fastafile, in);
while(!in.eof()){
if (m->getControl_pressed()) { break; }
Sequence currSeq(in); gobble(in);
string comment = " ";
if (useNameMap) {
itCount = nameMap.find(currSeq.getName());
if (itCount != nameMap.end()) {
comment += toString(itCount->second) + " ";
nameMap.erase(itCount);
}else { m->mothurOut("[ERROR]: Missing count data for " + currSeq.getName() + ", please correct.\n"); m->setControl_pressed(true); }
}
if (useTax) {
itTax = taxMap.find(currSeq.getName());
if (itTax != taxMap.end()) {
comment += itTax->second;
taxMap.erase(itTax);
}else { m->mothurOut("[ERROR]: Missing taxonomy for " + currSeq.getName() + ", please correct.\n"); m->setControl_pressed(true); }
}
currSeq.setComment(comment);
currSeq.printSequence(out);
}
in.close(); out.close();
return outputFileName;
}
catch(exception& e) {
m->errorOut(e, "MergeFileCommand", "mergeFileData");
exit(1);
}
}
//**********************************************************************************************************************
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